Cover Page

INTRODUCTION TO
BAYESIAN STATISTICS


Third Edition



WILLIAM M. BOLSTAD
JAMES M. CURRAN
















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This book is dedicated to

Sylvie,
Ben, Rachel,
Emily, Mary, and
Elizabeth

PREFACE

Our original goal for this book was to introduce Bayesian statistics at the earliest possible stage to students with a reasonable mathematical background. This entailed coverage of a similar range of topics as an introductory statistics text, but from a Bayesian perspective. The emphasis is on statistical inference. We wanted to show how Bayesian methods can be used for inference and how they compare favorably with the frequentist alternatives. This book is meant to be a good place to start the study of Bayesian statistics. From the many positive comments we have received from many users, we think the book succeeded in its goal. A course based on this goal would include Chapters 1-14.

Our feedback also showed that many users were taking up the book at a more intermediate level instead of the introductory level original envisaged. The topics covered in Chapters 2 and 3 would be old hat for these users, so we would have to include some more advanced material to cater for the needs of that group. The second edition aimed to meet this new goal as well as the original goal. We included more models, mainly with a single parameter. Nuisance parameters were dealt with using approximations. A course based on this goal would include Chapters 4-16.

Changes in the Third Edition

Later feedback showed that some readers with stronger mathematical and statistical background wanted the text to include more details on how to deal with multi-parameter models. The third edition contains four new chapters to satisfy this additional goal, along with some minor rewriting of the existing chapters. Chapter 17 covers Bayesian inference for Normal observations where we do not know either the mean or the variance. This chapter extends the ideas in Chapter 11, and also discusses the two sample case, which in turn allows the reader to consider inference on the difference between two means. Chapter 18 introduces the Multivariate Normal distribution, which we need in order to discuss multiple linear regression in Chapter 19. Finally, Chapter 20 takes the user beyond the kind of conjugate analysis is considered in most of the book, and into the realm of computational Bayesian inference. The covered topics in Chapter 20 have an intentional light touch, but still give the user valuable information and skills that will allow them to deal with different problems. We have included some new exercises and new computer exercises which use new Minitab macros and R-functions. The Minitab macros can be downloaded from the book website: http://introbayes.ac.nz. The new R functions have been incorporated in a new and improved version of the R package Bolstad, which can either be downloaded from a CRAN mirror or installed directly in R using the internet. Instructions on the use and installation of the Minitab macros and the Bolstad package in R are given in Appendices C and D respectively. Both of these appendices have been rewritten to accommodate changes in R and Minitab that have occurred since the second edition.

Our Perspective on Bayesian Statistics

A book can be characterized as much by what is left out as by what is included. This book is our attempt to show a coherent view of Bayesian statistics as a good way to do statistical inference. Details that are outside the scope of the text are included in footnotes. Here are some of our reasons behind our choice of the topics we either included or excluded.

In particular, we did not mention decision theory or loss functions when discussing Bayesian statistics. In many books, Bayesian statistics gets compartmentalized into decision theory while inference is presented in the frequentist manner. While decision theory is a very interesting topic in its own right, we want to present the case for Bayesian statistical inference, and did not want to get side-tracked.

We think that in order to get full benefit of Bayesian statistics, one really has to consider all priors subjective. They are either (1) a summary of what you believe or (2) a summary of all you allow yourself to believe initially. We consider the subjective prior as the relative weights given to each possible parameter value, before looking at the data. Even if we use a at prior to give all possible values equal prior weight, it is subjective since we chose it. In any case, it gives all values equal weight only in that parameterization, so it can be considered “objective” only in that parameterization. In this book we do not wish to dwell on the problems associated with trying to be objective in Bayesian statistics. We explain why universal objectivity is not possible (in a footnote since we do not want to distract the reader). We want to leave him/her with the “relative weight” idea of the prior in the parameterization in which they have the problem in.

In the first edition we did not mention Jeffreys' prior explicitly, although the beta prior for binomial and at prior for normal mean are in fact the Jeffreys' prior for those respective observation distributions. In the second edition we do mention Jeffreys' prior for binomial, Poisson, normal mean, and normal standard deviation. In third edition we mention the independent Jeffreys priors for normal mean and standard deviation. In particular, we don't want to get the reader involved with the problems about Jeffreys' prior, such as for mean and variance together, as opposed to independent Jeffreys' priors, or the Jeffreys' prior violating the likelihood principal. These are beyond the level we wish to go. We just want the reader to note the Jeffreys' prior in these cases as possible priors, the relative weights they give, when they may be appropriate, and how to use them. Mathematically, all parameterizations are equally valid; however, usually only the main one is very meaningful. We want the reader to focus on relative weights for their parameterization as the prior. It should be (a) a summary of their prior belief (conjugate prior matching their prior beliefs about moments or median), (b) at (hence objective) for their parameterization, or (c) some other form that gives reasonable weight over the whole range of possible values. The posteriors will be similar for all priors that have reasonable weight over the whole range of possible values.

The Bayesian inference on the standard deviation of the normal was done where the mean is considered a known parameter. The conjugate prior for the variance is the inverse chi-squared distribution. Our intuition is about the standard deviation, yet we are doing Bayes' theorem on the variance. This required introducing the change of variable formula for the prior density.

In the second edition we considered the mean as known. This avoided the mathematically more advanced case where both mean and standard deviation are unknown. In the third edition we now cover this topic in Chapter 17. In earlier editions the Student's t is presented as the required adjustment to credible intervals for the mean when the variance is estimated from the data. In the third edition we show in Chapter 17 that in fact this would be the result when the joint posterior found, and the variance marginalized out. Chapter 17 also covers inference on the difference in two means. This problem is made substantially harder when one relaxes the assumption that both populations have the same variance. Chapter 17 derives the Bayesian solution to the well-known Behrens-Fisher problem for the difference in two population means with unequal population variances. The function bayes.t.test in the R package for this book actually gives the user a numerical solution using Gibbs sampling. Gibbs sampling is covered in Chapter 20 of this new edition.

Acknowledgments

WMB would like to thank all the readers who have sent him comments and pointed out misprints in the first and second editions. These have been corrected. WMB would like to thank Cathy Akritas and Gonzalo Ovalles at Minitab for help in improving his Minitab macros. WMB and JMC would like to thank Jon Gurstelle, Steve Quigley, Sari Friedman, Allison McGinniss, and the team at John Wiley & Sons for their support.

Finally, last but not least, WMB wishes to thank his wife Sylvie for her constant love and support.

WILLIAM M. “BILL' BOLSTAD

Hamilton, New Zealand

JAMES M. CURRAN

Auckland, New Zealand